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treeducken
View on CRAN: Click
here
Download and install treeducken package within the R console
Install from CRAN:
install.packages("treeducken")
Install from Github:
library("remotes")
install_github("cran/treeducken") Install by package version:
library("remotes")
install_version("treeducken", "1.1.0") Attach the package and use:
library("treeducken")
Maintained by
Wade Dismukes
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-10-06
Latest Update:
Description:
Simulates nested phylogenetic trees (gene trees in species tree,
symbiont trees in host trees) using birth-death processes and transfers
between lineages. Simulations of gene trees within species trees are performed
using a three-tree model with species trees, locus trees, and gene trees.
The cophylogenetic birth-death process is used to simulate sets of host and
symbiont trees with extant associations between tips.
For more information about the three-tree model see:
Mallo et al. (2015) ,
Rasmussen and Kellis (2012) .
How to cite:
Wade Dismukes (2020). treeducken: Nested Phylogenetic Tree Simulator. R package version 1.1.0, https://cran.r-project.org/web/packages/treeducken. Accessed 12 Jun. 2026.
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Other R packages that treeducken depends,
imports, suggests or enhances
Functions, R codes and Examples using
the treeducken R package
Some associated functions: add_events . add_scalebar . build_historical_association_matrix . c.cophy . calculate_expected_leaves_locustree . calculate_expected_leaves_sptree . collapse_locus_subtree . convert_assoc_table_to_matrix . convert_to_cophy . cophy_summary_stat . count_cherries . draw_cophy . draw_curve . drop_extinct . estimate_node_heights . genetree_summary_stat . get_ana_events . get_loci . get_tip_labels_tree_list . is.cophy . is_extinct . make_textbox . parafit_stat . plot.cophy . print.cophy . retrieve_parent_genetrees . sim_cophyBD . sim_cophyBD_ana . sim_ltBD . sim_msc . sim_multilocus_coal . sim_stBD . sim_stBD_t . str.multiCophy . summary.cophy . treeducken-package .
Some associated R codes: RcppExports.R . build_historical_assoc_mat.R . calculate_cophylo_summary_stat.R . calculate_genetree_summary_stat.R . convert_assoc_tab_to_mat.R . convert_to_cophylo.R . deprecated_sim_functions.R . estimate_node_heights.R . is.cophylo.R . plot_cophy.R . sim_multilocus.R . summary_cophylo.R . utilities.R . Full treeducken package functions and examples
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